Re: [AMBER] Question about how a charged system can be simulated using PBC?

From: Jason Swails <>
Date: Sun, 8 Jun 2014 21:26:37 -0400

On Sun, Jun 8, 2014 at 6:27 AM, Dr. Vitaly Chaban <>

> That is an old story... Counter-charge is implicitly added in some PME
> implementations, so formally it is OK to forget about the absence of
> the counter-ion.
> You need PBC only if you need to control pressure, right? In all other
> cases, why not to go a bit non-traditional and simulate a cluster?

​But a cluster doesn't behave like bulk liquid. In a microsocopic drop the
size you can simulate with MD simulations, the surface area-to-volume ratio
will be immensely large (and water molecules at the surface behave quite
differently from water molecules in the bulk.​

Unless you want to model the behavior of a microscopic water drop, I would
be very wary of dropping PBC in the simulation...

All the best,

Jason M. Swails
Rutgers University
Postdoctoral Researcher
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Received on Sun Jun 08 2014 - 18:30:03 PDT
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